R: A Subset of the Choe et al. (2005) "Golden Spike" Experiment

choedata {st} | R Documentation

## A Subset of the Choe et al. (2005) “Golden Spike” Experiment

### Description

These data are expression levels for a subset of the genes investigated in the Choe et al. (2005) “Golden Spike” Affymetrix case-control experiment.

From the original data the 2,535 probe sets for spike-ins with ratio 1:1 were removed, leaving in total 11,475 genes with 3 replicates per group, and 1,331 known differentially expressed genes.

### Usage

    data(choedata)

### Format

`choe2.mat` is a matrix of dimension 6 times 11,475. It contains the samples in its rows and the genes in its columns.

`choe2.L` describes the case control-structure of the experiment, and `choe2.degenes` indicates the known differentially expressed genes. `choe2.symbol.name`, `choe2.probe.name`, and `choe2.mapping` provide additional information on the investigated genes.

### References

Choe, S. E., M. Boutros, A. M. Michelson, G. M. Church, and M. ~S. Halfon. 2005. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control data set. Genome Biology 6, R16.

### Examples

    # load st library
    library("st")

    # load data set
    data(choedata)

    # 6 samples, 11,475 genes
    dim(choe2.mat)

    # two groups (case vs. control
    choe2.L

    # 1,331 differentially expressed genes
    sum(choe2.degenes)

    # further information on genes
    choe2.symbol.name
    choe2.probe.name
    choe2.mapping

[Package st version 1.2.5 Index]